GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Halococcus hamelinensis 100A6

Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate WP_007690272.1 C447_RS01785 galactonate dehydratase

Query= metacyc::MONOMER-18070
         (393 letters)



>NCBI__GCF_000336675.1:WP_007690272.1
          Length = 384

 Score =  199 bits (507), Expect = 9e-56
 Identities = 130/390 (33%), Positives = 210/390 (53%), Gaps = 22/390 (5%)

Query: 1   MTKISEIEAYILGKEVTSAQWASLMVLVRVTTNDGRVGWGETVSALRAEAVANFVKKI-N 59
           MT+I + E Y +       +W    + + + T+DG VGWGE V   R++ VA  V+++ +
Sbjct: 1   MTEIVDYELYDV-----PPRW----LFLELETSDGLVGWGEPVVEGRSKTVAAAVEELLD 51

Query: 60  TVLKGNDVFNVEKNRLEWYKHDFNMTISLESTTAYSAVDIASWDIIGKELGAPLYKLLGG 119
             L G D   +E +    Y+  F     +   +A + +D A WDI GK  GAP+++LLGG
Sbjct: 52  NYLLGRDPNRIEDHWQAMYRGGFYRGGPI-LMSAIAGIDQALWDIKGKRFGAPVHELLGG 110

Query: 120 KTRDKVLVYANGWYQNCVKPEDFAEKAKEIVKMGYKALKFDPFGPYFNDISKKGLDIAEE 179
           + RD++ VY   W     +P D  E A E V+ G+ ALK +         S   ++ A E
Sbjct: 111 RARDRIRVYQ--WIGGD-RPADVGEAAAEQVEAGFSALKMNATPEIRRVDSPAAVEAAVE 167

Query: 180 RVKAVREAVGDNVDILIEHHGRFNANSAIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRN 239
           R+++VREAVG  V+I ++ HGR     A  +   LE + P+F+EEP+ P+  + L +  +
Sbjct: 168 RLRSVREAVGPEVEIGVDFHGRVTKPMAKRLVAALEPHEPMFVEEPVLPQHNDALAEIAS 227

Query: 240 NTSLRIALGERIINKQQALYFMKEGLVDFLQADLYRIGGVTETKKVVGIAETFDVQMAFH 299
           +T+  IA GER+ ++       ++G VD +Q DL   GG+TE KK+  +AE +DV +A H
Sbjct: 228 HTTTPIATGERMFSRWDYKEVFEDGTVDVIQPDLSHAGGITEVKKIAAMAEAYDVALAPH 287

Query: 300 NAQGPILNAVTLQFDAFIPNFLIQE-SFYDWFPSWKRELIYNGTP----IDNGYAIIPER 354
              GP+  A  +Q DA  PN LIQE S    +      L Y   P     ++G+  + + 
Sbjct: 288 CPLGPVALASCIQVDACSPNALIQEQSLNIHYNETSDVLDYLADPSVFEYEDGFVDVLDE 347

Query: 355 PGLGVEVNEKMLDSLKVKGEEYFNPEEPVW 384
           PGLG++++E+ +++   + EE  +   P+W
Sbjct: 348 PGLGIDLDEEYIEA---QSEEPVDWHNPIW 374


Lambda     K      H
   0.319    0.137    0.409 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 388
Number of extensions: 19
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 393
Length of database: 384
Length adjustment: 30
Effective length of query: 363
Effective length of database: 354
Effective search space:   128502
Effective search space used:   128502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory